Browsing by Author "Nunez-Lillo, Gerardo"

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    A First Omics Data Integration Approach in Hass Avocados to Evaluate Rootstock-Scion Interactions: From Aerial and Root Plant Growth to Fruit Development
    (2024) Nunez-Lillo, Gerardo; Ponce, Excequel; Beyer, Clemens P.; Alvaro, Juan E.; Meneses, Claudio; Pedreschi, Romina
    Grafting, the careful selection of rootstocks and scions, has played a crucial role maintaining Chilean avocado fruit quality standards in a scenario in which climate change and drought-related issues have considerably decreased avocado fruit production in the last fifteen years. The historical use of seedling rootstocks in Chile has experienced a recent shift towards clonal rootstocks, driven by the potential to produce more consistent and predictable crops. This research aims to compare Hass avocado plants grafted on Mexicola seedling and Dusa (R) clonal rootstocks in a soilless and protected system using (i) a differential expression analysis of root and leaf samples and (ii) a fruit transcriptomic and metabolomic integration analysis to improve our understanding of rootstock-scion interaction and its impact on avocado tree performance and fruit quality. The results demonstrated that no significant transcriptomic and metabolomic differences were identified at fruit level in the ready-to-eat (RTE) stage for Hass avocado fruit from both rootstocks. However, Hass avocados grafted on the clonal rootstock showed greater aerial growth and slightly increased fruit size than the seedling rootstock due to the enrichment of cell wall-remodeling genes as revealed in leaves and fruit at harvest stage.
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    A multiomics integrative analysis of color de-synchronization with softening of 'Hass' avocado fruit: A first insight into a complex physiological disorder
    (2023) Nunez-Lillo, Gerardo; Ponce, Excequel; Arancibia-Guerra, Camila; Carpentier, Sebastien; Carrasco-Pancorbo, Alegria; Olmo-Garcia, Lucia; Chirinos, Rosana; Campos, David; Campos-Vargas, Reinaldo; Meneses, Claudio; Pedreschi, Romina
    Exocarp color de-synchronization with softening of 'Hass' avocado is a relevant recurrent problem for the avocado supply chain. This study aimed to unravel the mechanisms driving this de-synchronization integrating omics datasets from avocado exocarp of different storage conditions and color phenotypes. In addition, we propose potential biomarkers to predict color synchronized/de-synchronized fruit. Integration of transcriptomics, proteomics and metabolomics and network analysis revealed eight transcription factors associated with differentially regulated genes between regular air (RA) and controlled atmosphere (CA) and twelve transcription factors related to avocado fruit color de-synchronization control in ready-to-eat stage. CA was positively correlated to auxins, ethylene, cytokinins and brassinosteroids-related genes, while RA was characterized by enrichment of cell wall remodeling and abscisic acid content associated genes. At ready-to-eat higher contents of flavonoids, abscisic acid and brassinosteroids were associated with color-softening synchronized avocados. In contrast, de-synchronized fruit revealed increases of jasmonic acid, salicylic acid and auxin levels.
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    Cell wall disassembly, metabolome and transcriptome analysis in sweet cherry fruit with induced surface pitting
    (2023) Ponce, Excequel; Nunez-Lillo, Gerardo; Bravo, Camila; Vidal, Juan; Tapia Reyes, Patricio; Meneses, Claudio; Pedreschi, Romina; Fuentealba, Claudia
    Surface pitting is the main quality problem that develops during prolonged storage of sweet cherries. It appears as one or more depressions on the surface of the fruit and is associated with the collapse of cells under the skin of the fruit. However, this physiological disorder is not shown in all cultivars with the same intensity. This research aims to analyze the cell wall disassembly of two cultivars displaying contrasting susceptibility to damage after pitting induction. In addition, we evaluated the metabolomic and transcriptomic changes in sweet cherries during cold storage. Our results show that damage to 'Sweetheart' fruit was more severe than damage to 'Bing' fruit. No differences were observed in the cell wall composition between nonpitted and pitted cherries; however, the varietal differences during cold storage were the most significant. The resistant cultivar 'Bing' showed a longer sidechain of RG-I; instead, 'Sweetheart' PME and PG activity was more marked at the beginning of cold storage. The metabolomics analysis revealed several compounds related to the abiotic stress response, such as 3O-coumaroyl-D-quinic acid, chlorogenic acid, GABA and beta-sitosterol. Furthermore, transcriptomics showed a higher expression of stress-related hormones in the susceptible cultivar and cell wall remodeling-related genes in the resistant cultivar. In conclusion, the contrasting susceptivity to surface pitting in sweet cherries can be attributed to the varietal response to cold storage rather than the mechanical stress of pitting induction.
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    Color desynchronization with softening of 'Hass' avocado: Targeted pigment, hormone and gene expression analysis
    (2022) Arancibia-Guerra, Camila; Nunez-Lillo, Gerardo; Caceres-Mella, Alejandro; Carrera, Esther; Meneses, Claudio; Kuhn, Nathalie; Pedreschi, Romina
    Main determinants of 'Hass' avocado quality and consumer acceptance are mesocarp firmness and skin color. Relevant producing and exporting countries have evidenced during the last seasons color desynchronization with softening at edible ripeness. The mechanisms driving this desynchronization are still unknown. Thus, this study aimed to provide a first deep insight into this problem by combining targeted pigment, hormone and gene expression analysis in avocado exocarp samples from different harvests and storage conditions. Results showed that color desynchronization was more pronounced in regular air (RA) condition and early harvest for all or-chards. Prolonged controlled atmosphere (CA) storage synchronized color development in all orchards analyzed. Chlorophylls and carotenoids did not decrease in content as the fruit reached the ready to eat stage but remained stable while total anthocyanins increased in all evaluated orchards. Total anthocyanins and abscisic acid were strongly and positively correlated with the "black color" phenotype. The other evaluated hormones (JA, IAA, SA, tZ, DHZ, iP) revealed negative correlations with the "black color" phenotype. Gene expression related to the ethylene biosynthesis pathway (PamACS, PamETR avocado gene orthologues) showed an up-regulation in fruit phenotyped as ready to eat (RTE) Green. In addition, the expression of the genes orthologues PamPAL, PamF3H and PamCHS was also positively correlated with anthocyanin content in the skin. Our results revealed that color desynchronization with softening of 'Hass' avocado is quite complex in terms of hormonal interplay and the role of storage conditions (RA vs CA). Thus, further studies need broader approaches such as the incorporation of omics studies to elucidate the physiological and molecular mechanisms driving color desynchronization.
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    Deciphering the behind blackspot exocarp disorder in avocado cv. Hass through a hormonal, transcriptional and metabolic integration approach
    (2024) Nunez-Lillo, Gerardo; Hernandez, Ignacia; Olmedo, Patricio; Ponce, Excequel; Arancibia-Guerra, Camila; Sepulveda, Laura; Carrasco-Pancorbo, Alegria; Beiro-Valenzuela, Maria Gemma; Carrera, Esther; Banos, Jorge; Campos, David; Meneses, Claudio; Pedreschi, Romina
    Avocado cv. Hass is an important sub-tropical crop with an increasing global demand. However, the avocado supply chain experiences significant fruit losses, particularly during the postharvest stage due to diseases and disorders that manifest after prolonged cold storage or the ready-to-eat stage. The blackspot exocarp disorder, which appears as brown or black blotches only after extended cold storage conditions, leads to substantial commercial losses for exported avocados. This research aimed to identify transcriptomic, metabolomic, and hormonal changes in avocado fruits affected by blackspot disorder, differentiating between the green and black exocarp tissues directly impacted by this physiological disorder. The results showed a correlation between the black-colored exocarp of blackspot affected fruits with high levels of gibberellins, cytokinins, jasmonic acid and salicylic acid hormones. Metabolically, these changes were accompanied by a high fatty acid content of oleate, palmitate and linoleate. Using a metabolic pathway reconstruction analysis, we integrated hormonal and metabolic data with transcriptomic information. This approach identified several genes involved in central carbon metabolism, long-chain fatty acid elongation, and jasmonate/salicylate biosynthesis pathways, as well as a possible accumulation of lignins due to a high expression of genes associated with the phenylpropanoid pathway in the black exocarp of blackspot-affected fruits. These findings suggest that blackspot disorder results from a combination of plant defense mechanisms triggered to strengthen the fruit exocarp tissue.
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    Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study
    (2023) Urra, Claudio; Sanhueza, Dayan; Pavez, Catalina; Tapia, Patricio; Nunez-Lillo, Gerardo; Minio, Andrea; Miossec, Matthieu; Blanco-Herrera, Francisca; Gainza, Felipe; Castro, Alvaro; Cantu, Dario; Meneses, Claudio
    Wine cultivars are available to growers in multiple clonal selections with agronomic and enological differences. Phenotypic differences between clones originated from somatic mutations that accrued over thousands of asexual propagation cycles. Genetic diversity between grape cultivars remains unexplored, and tools to discriminate unequivocally clones have been lacking. This study aimed to uncover genetic variations among a group of clonal selections of 4 important Vitis vinifera cultivars: Cabernet sauvignon, Sauvignon blanc, Chardonnay, and Merlot, and use this information to develop genetic markers to discriminate the clones of these cultivars. We sequenced with short-read sequencing technology the genomes of 18 clones, including biological replicates for a total of 46 genomes. Sequences were aligned to their respective cultivar's reference genome for variant calling. We used reference genomes of Cabernet sauvignon, Chardonnay, and Merlot and developed a de novo genome assembly of Sauvignon blanc using long-read sequencing. On average, 4 million variants were detected for each clone, with 74.2% being single nucleotide variants and 25.8% being small insertions or deletions (InDel). The frequency of these variants was consistent across all clones. From these variants, we validated 46 clonal markers using high-throughput amplicon sequencing for 77.7% of the evaluated clones, most of them small InDel. These results represent an advance in grapevine genotyping strategies and will benefit the viticulture industry for the characterization and identification of the plant material.
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    NAC072 Interacts with HB12, HAT9, and MYBR1 in a Temporal Regulatory Network Controlling Peach Fruit Development
    (2023) Nunez-Lillo, Gerardo; Zabala, Jose; Lillo-Carmona, Victoria; Alvarez, Jose Miguel; Pedreschi, Romina; Meneses, Claudio
    Fruit development is a complex process that involves the interplay of different biological processes carefully coordinated to control fruit quality traits. The peach fruit development consists in four recognized growth stages (S1-S4). The second stage (S2) is characterized by the endocarp hardening process and is followed by the second exponential growth phase (S3), where an increase in fruit size is produced by a rapid cell expansion. A nectarine genotype incapable of ripening and described as a slow ripening phenotype was identified and selected as a good model for studying peach fruit development. Slow ripening fruit remained firm, green, and exhibited no rise in CO2 or ethylene production rates blocking fruit development at S3 stage. The transcription factor NAC072 has been proposed as a key regulatory element involved in both the slow ripening and the harvest date phenotypes. However, the regulatory mechanisms by which NAC072 produces these phenotypic changes are still unknown. Using a transcriptomic approach between normal and slow ripening individuals with a transcription factor-gene target interaction database, a NAC072 regulatory network was constructed, identifying putative direct and indirect NAC072 fruit development-related elements. Three transcription factors were identified along with NAC072 in early stages of fruit development, two homeobox-leucine zippers (HB12 and HAT9), and one MYB transcription factor (MYBR1). In addition, we determined that the NAC072 transcriptional regulatory network promotes phenylpropanoids biosynthesis and cell wall remodeling to develop fruit growth, seed development, and softening, probably through hormonal signaling pathways involving abscisic acid and gibberellic acid.
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    Proteomic and metabolomic integration reveals the effects of pre-flowering cytokinin applications on central carbon metabolism in table grape berries
    (2023) Olmedo, Patricio; Nunez-Lillo, Gerardo; Vidal, Juan; Leiva, Carol; Rojas, Barbara; Sagredo, Karen; Arriagada, Cesar; Defilippi, Bruno G.; Perez-Donoso, Alonso G.; Meneses, Claudio; Carpentier, Sebastien; Pedreschi, Romina; Campos-Vargas, Reinaldo
    Consumers around the world prefer high quality table grapes. To achieve higher quality traits at ripening, grapevine producers apply different plant growth regulators. The synthetic cytokinin forchlorfenuron N- (2-chloro-4-pyridinyl)-N '-phenylurea (CPPU) is widely used, its effect on grape quality is poorly understood. We hypothesized that the use of CPPU in pre-flowering can lead to changes in the metabolism that affects grape quality at harvest. Therefore, we investigated the role of CPPU applications on the quality of grapes by inte-grating proteomics and metabolomics. CPPU-treated grapevines showed a significant increase in berry size and firmness. Proteomic analyses indicated that CPPU-treated berries accumulated enzymes associated with carbo-hydrate metabolism, glycolysis, and tricarboxylic acid (TCA) cycle at harvest. Metabolomic analyses showed shifts in the abundance of compounds associated with carbohydrate metabolism and TCA cycle in CPPU-treated grapes. These findings suggest that CPPU applications modulate central carbon metabolism, improving grape berry quality.
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    Proteomics analysis reveals new insights into surface pitting of sweet cherry cultivars displaying contrasting susceptibility
    (2022) Nunez-Lillo, Gerardo; Ponce, Excequel; Alvaro, Juan E.; Campos, David; Meneses, Claudio; Campos-Vargas, Reinaldo; Carpentier, Sebastien; Fuentealba, Claudia; Pedreschi, Romina
    Surface pitting in sweet cherry (Prunus avium L.) is characterised by depressions development on the skin surface. Pitting damage happens during harvest and postharvest handling and develops during cold storage. This study compared two cultivars with contrasting susceptibility to pitting (Kordia: tolerant; Sweetheart: susceptible) using a LC-MS/MS proteomic approach to identify key metabolic and signalling pathways related to this disorder during ripening and postharvest storage. The variability observed in the principal component analysis was driven by the cultivars suggesting that surface pitting susceptibility is triggered by the inherent differences between cultivars. Proteins involved in anthocyanin biosynthesis were more abundant in Kordia. Moreover, CCR (cinnamoyl-CoA reductase) and FLS (flavonol synthase) proteins showed higher abundance in Sweetheart. An overexpression in enzymes related to the synthesis of abscisic acid (ABA), jasmonic acid (JA) and ethylene were found in Kordia. A higher abundance of sucrose synthase (SUS), UDP-glycosyltransferases (UDP-GT) and polygalacturonase-inhibiting proteins (PGIP) were observed in Kordia, while a higher content of invertase (INV) was observed in Sweetheart. The overexpression of the studied pathways suggests that tolerance to surface pitting could be correlated to one or more of these factors, and susceptibility might be given by the inherent differences in the metabolic processes of each cultivar.
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    Transcriptome and Gene Regulatory Network Analyses Reveal New Transcription Factors in Mature Fruit Associated with Harvest Date in Prunus persica
    (2022) Nunez-Lillo, Gerardo; Perez-Reyes, Wellasmin; Riveros, Anibal; Lillo-Carmona, Victoria; Rothkegel, Karin; Miguel Alvarez, Jose; Blanco-Herrera, Francisca; Pedreschi, Romina; Campos-Vargas, Reinaldo; Meneses, Claudio
    Harvest date is a critical parameter for producers and consumers regarding agro-industrial performance. It involves a pleiotropic effect controlling the development of other fruit quality traits through finely controlling regulatory mechanisms. Fruit ripening is a process in which various signals and biological events co-occur and are regulated by hormone signaling that produces the accumulation/degradation of multiple compounds. However, the regulatory mechanisms that control the hormone signaling involved in fruit development and ripening are still unclear. To investigate the issue, we used individuals with early, middle and late harvest dates from a peach segregating population to identify regulatory candidate genes controlling fruit quality traits at the harvest stage and validate them in contrasting peach varieties for this trait. We identified 467 and 654 differentially expressed genes for early and late harvest through a transcriptomic approach. In addition, using the Arabidopsis DAP-seq database and network analysis, six transcription factors were selected. Our results suggest significant hormonal balance and cell wall composition/structure differences between early and late harvest samples. Thus, we propose that higher expression levels of the transcription factors HB7, ERF017 and WRKY70 in early harvest individuals would induce the expression of genes associated with the jasmonic acid pathway, photosynthesis and gibberellins inhibition. While on the other hand, the high expression levels of LHY, CDF3 and NAC083 in late harvest individuals would promote the induction of genes associated with abscisic acid biosynthesis, auxins and cell wall remodeling.